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对树木概念进行分类:树的树。

Categorizing ideas about trees: a tree of trees.

机构信息

URM 7138 CNRS-MNHN-UPMC-IRD Systématique, Adaptation, Evolution, Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, France.

出版信息

PLoS One. 2013 Aug 7;8(8):e68814. doi: 10.1371/journal.pone.0068814. eCollection 2013.

DOI:10.1371/journal.pone.0068814
PMID:23950877
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3737276/
Abstract

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a "tree of trees." Then, we categorize schools of tree-representations. Classical schools like "cladists" and "pheneticists" are recovered but others are not: "gradists" are separated into two blocks, one of them being called here "grade theoreticians." We propose new interesting categories like the "buffonian school," the "metaphoricians," and those using "strictly genealogical classifications." We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.

摘要

本研究旨在探讨用于生成生物系统分类的矩阵和 MP 树是否可用于生成科学史中的思想分类。我们研究了系统学中树的使用历史,以代表从 1766 年到 1991 年生命的多样性。我们将受同源生物部分编码启发的方法应用于这些思想。我们将关于树的思想、著作和绘图中的概念部分进行离散化,将 41 篇主要著作中的概念部分进行离散化;我们检测作者之间的共享部分,并将其编码为 91 个字符的矩阵,并使用树状图来显示谁与谁共享什么。换句话说,我们提出了一种作者之间关于树的共享思想的分层表示:这产生了一个“树的树”。然后,我们对树表示的学派进行分类。恢复了经典学派,如“分支学派”和“形态学派”,但其他学派则没有:“梯度学派”分为两个块,其中一个在此称为“梯度理论家”。我们提出了一些新的有趣的类别,如“布丰学派”、“隐喻学派”以及那些使用“严格的谱系分类”的学派。我们认为,在目前的研究阶段,网络不适用于表示共享思想。我们制作了一个分支图,以显示谁与谁共享什么,同时还显示了特征的异源性和同功性。目前的分支图并未对树的思想传播过程进行建模,主要用于检验具有相同年龄的思想的接近程度和分类。

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引用本文的文献

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PLoS One. 2020 Jan 15;15(1):e0226567. doi: 10.1371/journal.pone.0226567. eCollection 2020.
2
The Evolution of Musical Diversity: The Key Role of Vertical Transmission.音乐多样性的演变:垂直传播的关键作用。
PLoS One. 2016 Mar 30;11(3):e0151570. doi: 10.1371/journal.pone.0151570. eCollection 2016.

本文引用的文献

1
CLADISTICS OF CLADISTS.支序分类学家的支序分类学
Cladistics. 1987 Dec;3(4):363-375. doi: 10.1111/j.1096-0031.1987.tb00899.x.
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Trees and networks before and after Darwin.达尔文之前和之后的树木和网络。
Biol Direct. 2009 Nov 16;4:43; discussion 43. doi: 10.1186/1745-6150-4-43.
3
Trees of trees: an approach to comparing multiple alternative phylogenies.树之树:一种比较多个备选系统发育树的方法。
Syst Biol. 2008 Oct;57(5):785-94. doi: 10.1080/10635150802424072.
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Ordering events of biochemical evolution.生物化学进化的有序事件。
Biochimie. 2007 May;89(5):555-73. doi: 10.1016/j.biochi.2006.12.007. Epub 2007 Jan 4.
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A phylogenetic approach to cultural evolution.一种研究文化进化的系统发育方法。
Trends Ecol Evol. 2005 Mar;20(3):116-21. doi: 10.1016/j.tree.2004.12.002. Epub 2004 Dec 24.
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Application of phylogenetic networks in evolutionary studies.系统发育网络在进化研究中的应用。
Mol Biol Evol. 2006 Feb;23(2):254-67. doi: 10.1093/molbev/msj030. Epub 2005 Oct 12.
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Integrating the universal metabolism into a phylogenetic analysis.将通用代谢整合到系统发育分析中。
Mol Biol Evol. 2005 Jan;22(1):1-11. doi: 10.1093/molbev/msh253. Epub 2004 Sep 8.
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Evolution of amino acid metabolism inferred through cladistic analysis.
J Biol Chem. 2003 Nov 28;278(48):47960-70. doi: 10.1074/jbc.M213028200. Epub 2003 Aug 29.
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The roots of phylogeny: how did Haeckel build his trees?系统发育学的根源:海克尔是如何构建他的进化树的?
Syst Biol. 2003 Aug;52(4):515-27. doi: 10.1080/10635150390218277.
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Early steps of metabolism evolution inferred by cladistic analysis of amino acid catabolic pathways.
C R Biol. 2002 Feb;325(2):119-29. doi: 10.1016/s1631-0691(02)01411-7.